1tbk

From Proteopedia

Revision as of 23:50, 24 November 2007

NMR structure of the VS ribozyme stem-loop V RNA in the absence of multivalent ions.

Overview

An important step in the substrate recognition of the Neurospora Varkud, Satellite (VS) ribozyme is the formation of a magnesium-dependent, loop/loop interaction between the terminal loops of stem-loops I and V. We, have studied the structure of stem-loop V by nuclear magnetic resonance, spectroscopy and shown that it adopts a U-turn conformation, a common, motif found in RNA. Structural comparisons indicate that the U-turn of, stem-loop V fulfills some but not all of the structural characteristics, found in canonical U-turn structures. This U-turn conformation exposes the, Watson-Crick faces of the bases within stem-loop V (G697, A698, and C699), and makes them accessible for interaction with stem-loop I. Using, chemical-shift mapping, we show that magnesium ions interact with the loop, of the isolated stem-loop V and induce a conformational change that may be, important for interaction with stem-loop I. This study expands our, understanding of the role of U-turn motifs in RNA structure and function, and provides insights into the mechanism of substrate recognition in the, VS ribozyme.

About this Structure

1TBK is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

Reference

Nuclear magnetic resonance structure of the Varkud satellite ribozyme stem-loop V RNA and magnesium-ion binding from chemical-shift mapping., Campbell DO, Legault P, Biochemistry. 2005 Mar 22;44(11):4157-70. PMID:15766243

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